updated validation logic for user provided checkm2 database and relavent param names.

Author: Y-Pei

nextflow.config

@@ -19,8 +19,8 @@ params {
     upload_force               = true
     test_upload                = true
     webincli_submit            = true
-    db_zenodo_id               = '14897628'
-    db_zenodo_path             = null
+    checkm2_db_zenodo_id       = '14897628'
+    checkm2_db_zenodo_path     = null
 
     // MultiQC options
     multiqc_config             = null

nextflow_schema.json

@@ -264,11 +264,11 @@
         }
     ],
     "properties": {
-        "db_zenodo_id": {
+        "checkm2_db_zenodo_id": {
             "type": "string",
             "default": 14897628
         },
-        "db_zenodo_path": {
+        "checkm2_db_zenodo_path": {
             "type": "string"
         }
     }

workflows/genomesubmit.nf

@@ -40,16 +40,15 @@ workflow GENOMESUBMIT {
         complete: !checkM2_missing
     }
     // Run checkM2 database download if any completeness/contamination values are missing & no db path provided
-    if (params.db_zenodo_path == null) {
-        CHECKM2_DATABASEDOWNLOAD(params.db_zenodo_id)
+    if (!params.checkm2_db_zenodo_path || !file(params.checkm2_db_zenodo_path).exists()) {
+        CHECKM2_DATABASEDOWNLOAD(params.checkm2_db_zenodo_id)
         ch_check2_db = CHECKM2_DATABASEDOWNLOAD.out.database
     }
     else {
-        // Create a tuple that matches the expected structure from CHECKM2_DATABASEDOWNLOAD
         ch_check2_db = Channel.of(
             [
                 [id: "db_zenodo_meta"],
-                file(params.db_zenodo_path),
+                file(params.checkm2_db_zenodo_path),
             ]
         )
     }